For 25 years I was the controller of a California corporation that owned a chain of bookstores. Every month I had to fill out the State sales tax report and pay California the sales tax due. The report called for total gross sales plus a breakout of the types of sales (Taxable, and non-taxable), location of sales, etc.
The Watchtower likes to keep it's financial data secret. But if they were required to pay sales taxes, they would have to report their book and magazine sales to the different States, provinces, and localities. There would be a public record of that Watchtower was making money off the sale of their publications, something the JW leaders don't want the public or the membership to know.
You are right that the Watchtower would have been wiser to have kept the fixed price for their publications and paid the sales tax like any legitimate business. Something the Watchtower is not. So to keep their financials a secret they bit the bullet and lost money.
I should mention that the prices the Watchtower was charging the JWs for their books and magazines prior to 1990, was what a for-profit printer that used union labor, would charge a secular book publisher for similar items. Plus the Watchtower had a captive audience for their publications. A secular publisher takes a risk with publishing a book. Not all books published become best sellers and many lose money.